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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 1vs6:B3008, See in JSmolMgRNA representative site for type cis-2OP-NB     Click on the image to toggle views


Site type: cis-2Oph·Nb

Schematic drawing for
cis-2Oph·Nb

MgRNA type cis-2OP-NB
List of all 118 Mg2+ binding sites with the site type cis-2Oph·Nb in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
Page 1 of 5 | « Previous | | 1 | 2 | 3 | 4 | 5
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1jj2 08089 cis-2Oph·Nb A:0516(OP1), U:0517(OP2) G:0518(N7) 07398, 07449, 07450
1k73 A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7862, A7912, A7913
1k73 A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A3606, A3612, A3623 G:A164, A:A165 G:A164
1k8a A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A3201, A3207, A3219 G:A164, A:A165 G:A164
1k9m A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A3603, A3609, A3620 G:A164, A:A165 G:A164
1kc8 A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7850, A7900, A7901 C:A515
1kc8 A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A3614, A3620, A3633 G:A164, A:A165 G:A164
1kd1 A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A3606, A3612, A3624 G:A164, A:A165 G:A164
1kd1 A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7848, A7898, A7899
1kqs 08089 cis-2Oph·Nb A:0516(OP1), U:0517(OP2) G:0518(N7) 07333, 07382, 07383 C:0515
1kqs 08079 cis-2Oph·Nb A:0167(OP1), C:0168(OP2) A:0165(N7) 03118, 03124, 03137 G:0164, A:0165 G:0164
1m1k A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7439, A7486, A7487
1m90 A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7381, A7431, A7432 C:A515
1n8r A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A8405, A8454, A8455 C:A515
1n8r A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A4006, A4012, A4024 G:A164, A:A165 G:A164
1nji A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7843, A7896, A7897 C:A515
1q81 A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7332, A7381, A7382
1q81 A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A3122, A3128, A3141 G:A164, A:A165 G:A164
1q82 A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A3123, A3129, A3141 G:A164, A:A165 G:A164
1q82 A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7322, A7370, A7371
1q86 A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7353, A7401, A7402
1q86 A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A3136, A3142, A3154 G:A164, A:A165 G:A164
1qvf 08089 cis-2Oph·Nb A:0516(OP1), U:0517(OP2) G:0518(N7) 07298, 07346, 07347
1qvg 08079 cis-2Oph·Nb A:0167(OP1), C:0168(OP2) A:0165(N7) 03116, 03122, 03133 G:0164, A:0165 G:0164
1qvg 08089 cis-2Oph·Nb A:0516(OP1), U:0517(OP2) G:0518(N7) 07231, 07276, 07277

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
used for Mg2+
"Site type"
Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen
cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform
Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].


Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>